Experiment: 9H1T

Crystal structure of apo-tyrosinase from Priestia megaterium F227Y mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NM8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	295.15	0.1 M magnesium formate dihydrate, 15% PEG 3500

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.894	α = 90
b = 78.631	β = 103.973
c = 86.587	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS EIGER X 4M		2022-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.14	57.43	96.69	0.825	7.6	1.9		33209

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.14	2.22	97.3		0.804	4.3	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.14	40.01	1.34	33198	1702	96.57	0.2079	0.2038	0.2826	19.43

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.8034
f_angle_d	0.9549
f_chiral_restr	0.0512
f_plane_restr	0.0096
f_bond_d	0.0073

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4656
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
XDS	data reduction
Aimless	data scaling